Uprooting phylogenetic uncertainty in coalescent species delimitation: A meta-analysis of empirical studies

Itzue W. Caviedes-Solis*, Nassima M. Bouzid, Barbara L. Banbury, Adam D. Leaché

*Corresponding author for this work

Research output: Journal PublicationsJournal Article (refereed)peer-review

14 Citations (Scopus)


Phylogenetic and phylogeographic studies rely on the accurate quantification of biodiversity. In recent studies of taxonomically ambiguous groups, species boundaries are often determined based on multi-locus sequence data. Bayesian Phylogenetics and Phylogeography (BPP) is a coalescent-based method frequently used to delimit species; however, empirical studies suggest that the requirement of a user-specified guide tree biases the range of possible outcomes. We evaluate fifteen multi-locus datasets using the most recent iteration of BPP, which eliminates the need for a user-specified guide tree and reconstructs the species tree in synchrony with species delimitation (= unguided species delimitation). We found that the number of species recovered with guided versus unguided species delimitation was the same except for two cases, and that posterior probabilities were generally lower for the unguided analyses as a result of searching across species trees in addition to species delimitation models. The guide trees used in previous studies were often discordant with the species tree topologies estimated by BPP. We also compared species trees estimated using BPP and *BEAST and found that when the topologies are the same, BPP tends to give higher posterior probabilities.

Original languageEnglish
Pages (from-to)866-873
Number of pages8
JournalCurrent Zoology
Issue number5
Publication statusPublished - 1 Jan 2015
Externally publishedYes


  • BPP
  • Phylogeography
  • Species delimitation
  • Species tree


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